User:Adam Meade/Sandbox 1

Iron Response Regulator (Irr)

=Background Information= Iron is potentially toxic to cells, as in the presence of oxygen, Fenton reactions can produce reactive oxygen species that can destroy essential biomolecules. Balancing the amount of iron in the cell is important and this importance is apparent from the elaborate mechanisms cells devote to iron homeostasis. Part of this iron balancing is achieved by regulation of iron import. The genes required for ferric citrate transport in Rhodobacter sphaeroides form a cluster in the order fecI-fecR-fecABCDE, encoding a specialized sigma factor and a putative anti-sigma factor that together are responsible for regulated transcription of the ferric citrate transport operon, encoding an ABC-type ferric citrate transporter. In Escherichia coli, fecI transcription is regulated by Fur in response to iron availability; in Bradyrhizobium japonicum, as well as R. sphaeroides, which both lack Fur, fecI transcription is thought to be regulated by another iron-responsive DNA binding protein, Irr, or the iron response regulator protein, which can also be considered to be a relative to the family of Fur proteins.

=Irr and Other Iron-Regulating Proteins= Since there are bacteria that have to have iron level-mediating proteins present but do not have the Fur (ferric uptake regulator) protein, there must be another protein that takes its place. In the case of B. japonicum, which does not have the Fur protein, the Irr protein was found to be the regulator of iron levels within the cell.

=Function of Irr= Irr behaves differently than other regulatory proteins. To prevent the accumulation of toxic porphyrin precursors under iron limitation, as when iron is limiting, heme cannot be produced.

Irr accumulates in cells under iron limitation, with very low levels of Irr being present in iron-replete cells. This is a distinction when compared to other Fur family proteins because it functions in the absence of the regulatory metal, whereas the other members require direct metal-binding for the protein to be activated.

=Phylogenetic Tree=

http://consurf.tau.ac.il/results/1240766462/treeView.html

=Chemical and Physical Properties of Irr=

Molecular weight: 18338.8 Da

Theoretical pI: 6.03

=Evolution of Irr/Fur=

Amino Acid Conservation Scores

The following are scores on how well conserved the amino acids are in relation to proteins with a similar structure to Irr. This could potentially show us where Irr evolved from/what Irr will evolve into.

- POS: The position of the AA in the SEQRES derived sequence.

- SEQ: The SEQRES derived sequence in one letter code.

- COLOR: The color scale representing the conservation scores (9 - conserved, 1 - variable).

- RESIDUE VARIETY: The residues variety at each position of the multiple sequence alignment.

POS	 SEQ	   COLOR	RESIDUE VARIETY (normalized) 1	  D	      9	         D                    2	   V	      2*         F,N,V,Y 3	  N	      6	         A,N,S,T 4	  E	      3*	 E,G,K,Q,S,T 5	  M	      3*	 A,E,I,L,M,Q,T 6	  L	      9	         L                    7	   Q	      7          K,Q,R 8	  S	      1          D,E,K,N,Q,R,S,T 9	  A	      5	         A,G,I,M,N,S,T,V 10	  G	      8          D,G 11	  L	      8          I,L,V 12	  R	      8	         K,R 13	  P	      4          A,I,P,V,Y 14	  T	      9          T                   15	   R	      3*	 E,F,G,K,L,P,R,V 16	  Q	      8	         P,Q 17	  R	      9          R                   18	   M	      3*	 E,H,I,L,M,Q,V 19	  A	      8          A,K,T,V 20	  L	      7          I,L,V 21	  G	      6          G,I,L,M 22	  W	      1          A,D,E,K,N,Q,R,W 23	  L	      1          A,F,I,L,M,T,V,Y 24	  L	      7          F,L,M,V 25	  F	      1	         D,E,F,I,K,N,Q,R,V,Y 26	  G	      1	         A,E,G,H,K,N,Q,S,T 27	  K	      3*	 A,E,H,K,P,S,T 28	  G	      1	         A,D,E,G,H,K,M,P,R 29	  A	      1	         A,C,E,G,L,M,N,Q,S,T 30	  R	      1	         E,H,Q,R 31	  H	      9	         H                   32	   L	      3*	 A,F,I,L,M,P,V,Y 33	  T	      8	         D,E,S,T 34	  A	      9	         A,P,T 35	  E	      8	         D,E 36	  M	      3*	 A,D,E,H,M,S,T 37	  L	      5	         C,I,L,V 38	  Y	      7	         F,I,Y 39	  E	      5	         E,G,K,M,N,Q,R 40	  E	      1	         A,E,H,I,K,L,R 41	  A	      6	         A,F,I,L,V 42	  T	      2	         A,E,I,L,M,R,S,T 43	  L	      1	         A,D,E,F,G,L,N,P,S,V 44	  A	      1	         A,D,E,I,K,L,M,P,Q,R,S 45	  K	      1	         D,F,G,H,K,L,N,S 46	  V	      3*	 C,E,L,M,P,S,V 47	  P	      4	         D,E,N,P 48	  V	      7	         I,M,V 49	  S	      9	         G,S 50	  L	      5	         H,I,L,R,V 51	  A	      9	         A,Q,S 52	  T	      9	         A,T 53	  V	      8	         I,V 54	  Y	      9	         Y                   55	   N	      8	         D,N,R 56	  T	      8	         N,T,V,X 57	  L	      9	         L                   58	   N	      7	         H,K,N,R,T 59	  Q	      7	         A,L,Q,V 60	  L	      7	         F,L,M 61	  T	      5	         A,D,E,K,R,T 62	  D	      4	         A,D,E,Q,R,S 63	  A	      7	         A,I,M,S,V 64	  G	      8	         E,G,H 65	  L	      6	         I,L,M 66	  L	      7	         L,V 67	  R	      4	         I,K,L,Q,R,S,T,V 68	  Q	      6	         E,K,Q,R,S 69	  V	      5	         H,I,L,N,S,V 70	  S	      5	         D,H,N,P,Q,S,T 71	  V	      5	         F,L,P,V,Y 72	  D	      2	         A,D,E,G,S,T 73	  G	      5	         D,E,G,S,T 74	  T	      5	         A,D,G,N,S,T 75	  K	      5	         G,H,K,S,V 76	  T	      6	         A,K,S,T 77	  Y	      6	         H,I,K,R,V,Y 78	  F	      6	         F,Y 79	  D	      8	         D,E 80	  T	      6	         F,L,S,T 81	  N	      3	         A,D,N,R,S,T,V 82	  V	      4*	 Q,V 83	  T	      1	         D,E,K,N,P,Q,T,V 84	  T	      1	         D,G,K,L,N,Q,S,T 85	  H	      1	         D,E,G,H,K,P,S 86	  H	      8	         D,E,H,N 87	  H	      9	         H                   88	   Y	      8	         D,H,Y 89	  Y	      9          H,Y 90	  L	      2	         A,I,L,M,V 91	  E	      1	         E,K,L,M,T,V 92	  N	      2*	 D,E,K,N,Q,V 93	  S	      7	         C,S,T 94	  H	      5	         G,H,N,S 95	  E	      6	         E,K,T 96	  L	      8	         I,L,V 97	  V	      6	         F,I,T,V 98	  D	      8	         D,E 99	  I	      8	         F,I 100	  E	      1	         E,H,K,M,Q,S,T 101	  D	      6	         D,N,S,Y 102	  P	      6	         A,E,N,P 103	  H	      1	         D,E,G,H,I,Q,V 104	  L	      8	         I,L 105	  A	      3*	 A,K,Q 106	  L	      5*	 L,R 107	  S	      7	         Q,S 108	  K	      3*	 D,K,R 109	  M	      4*	 E,K,M 110	  P	      7	         I,P 111	  E	      4*	 A,E,S,V 112	  V	      2*	 A,E,R,V 113	  P	      3*	 E,K,P,Q 114	  E	      1	         E,H,N,R,Y 115	  G	      7	         G,N 116	  Y	      2	         F,I,V,Y 117	  E	      5*	 E,R 118	  I	      6*	 I,L 119	  A	      6*	 A,V 120	  R	      4*	 D,R 121	  I	      4*	 H,I 122	  D	      6*	 D,N 123	  M	      6*	 L,M 124	  V	      8*	 V                  125	   V	      5*	 L,V 126	  R	      4*	 R,Y 127	  L	      6*	 L,V 128	  R	      8*	 R                  129	   K	      8*	 K                  130	   K	      8*	 K                  131	   R	      6*	 K,R

=Structure of the Proposed Irr Protein=



Secondary Structure

Polar/Hydrophobic Regions

Amino terminus to carboxy terminus

The amino acid sequence used to derive the structure shown is as follows:

1 msentaphhd ddvhaaalls grqpaltgcp whdvnemlqs aglrptrqrm algwllfgkg

61 arhltaemly eeatlakvpv slatvyntln qltdagllrq vsvdgtktyf dtnvtthhhy

121 ylenshelvd iedphlalsk mpevpegyei aridmvvrlr kkr

=References=

HOW WAS THE ANIMATED IMAGE GENERATED?

1. Go to the POLYVIEW 3D homepage, http://polyview.cchmc.org/polyview3d.html

2. On the submission form, first select 'animation' in the "type of request" section, select the size of the animation to be generated in pixels(here the size is 600), then upload the PDB format protein structure file in the "source of structural data" section.

3. On the "chain color and rendering section" select 'cartoon' and 'secondary structure'.

4. On "advanced structural annotation" section select 'docking models in Capri format'.

5. Any other forms for the animation may be selected by referring to the "Samples" according to the protein structure to be animated.

HOW WAS THE JMOL IMAGE GENERATED?

1. First retrieve your protein sequence from http://www.ncbi.nlm.nih.gov/.

2. Go to 3D-JIGSAW page http://bmm.cancerresearchuk.org/~3djigsaw/ and paste the sequence on the submission page. A .pdb format image of your protein will be sent to you on your email which can be opened by RASMOL.

3. Upload this file on Proteopedia and then load the JMol applet for the protein following instructions on the Help:Editing page http://www.proteopedia.org/wiki/index.php/Help:Editing.

4. You can edit your protein by using the scene authoring tools after loading the applet.